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1.  Enhanced Specificity of TPMT*2 Genotyping Using Unidirectional Wild-Type and Mutant Allele-Specific Scorpion Primers in a Single Tube 
PLoS ONE  2014;9(4):e91824.
Genotyping of thiopurine S-methyltransferase (TPMT) is recommended for predicting the adverse drug response of thiopurines. In the current study, a novel version of allele-specific PCR (AS-PCR), termed competitive real-time fluorescent AS-PCR (CRAS-PCR) was developed to analyze the TPMT*2 genotype in ethnic Chinese. This technique simultaneously uses wild-type and mutant allele-specific scorpion primers in a single reaction. To determine the optimal conditions for both traditional AS-PCR and CRAS-PCR, we used the Taguchi method, an engineering optimization process that balances the concentrations of all components using an orthogonal array rather than a factorial array. Instead of running up to 264 experiments with the conventional factorial method, the Taguchi method achieved the same optimization using only 16 experiments. The optimized CRAS-PCR system completely avoided non-specific amplification occurring in traditional AS-PCR and could be performed at much more relaxed reaction conditions at 1% sensitivity, similar to traditional AS-PCR. TPMT*2 genotyping of 240 clinical samples was consistent with published data. In conclusion, CRAS-PCR is a novel and robust genotyping method, and the Taguchi method is an effective tool for the optimization of molecular analysis techniques.
doi:10.1371/journal.pone.0091824
PMCID: PMC3976262  PMID: 24705376
2.  BRAFV600E Mutation and Its Association with Clinicopathological Features of Colorectal Cancer: A Systematic Review and Meta-Analysis 
PLoS ONE  2014;9(3):e90607.
Background
Colorectal cancer (CRC) is a heterogeneous disease with multiple underlying causative genetic mutations. The B-type Raf proto-oncogene (BRAF) plays an important role in the mitogen-activated protein kinase (MAPK) signaling cascade during CRC. The presence of BRAFV600E mutation can determine the response of a tumor to chemotherapy. However, the association between the BRAFV600E mutation and the clinicopathological features of CRC remains controversial. We performed a systematic review and meta-analysis to estimate the effect of BRAFV600E mutation on the clinicopathological characteristics of CRC.
Methods
We identified studies that examined the effect of BRAFV600E mutation on CRC within the PubMed, ISI Science Citation Index, and Embase databases. The effect of BRAFV600E on outcome parameters was estimated by odds ratios (ORs) with 95% confidence intervals (CIs) for each study using a fixed effects or random effects model.
Results
25 studies with a total of 11,955 CRC patients met inclusion criteria. The rate of BRAFV600 was 10.8% (1288/11955). The BRAFV600E mutation in CRC was associated with advanced TNM stage, poor differentiation, mucinous histology, microsatellite instability (MSI), CpG island methylator phenotype (CIMP). This mutation was also associated with female gender, older age, proximal colon, and mutL homolog 1 (MLH1) methylation.
Conclusions
This meta-analysis demonstrated that BRAFV600E mutation was significantly correlated with adverse pathological features of CRC and distinct clinical characteristics. These data suggest that BRAFV600E mutation could be used to supplement standard clinical and pathological staging for the better management of individual CRC patients, and could be considered as a poor prognostic marker for CRC.
doi:10.1371/journal.pone.0090607
PMCID: PMC3940924  PMID: 24594804
3.  High-Resolution Melting Analysis for accurate detection of BRAF mutations: a systematic review and meta-analysis 
Scientific Reports  2014;4:4168.
The high-resolution melting curve analysis (HRMA) might be a good alternative method for rapid detection of BRAF mutations. However, the accuracy of HRMA in detection of BRAF mutations has not been systematically evaluated. We performed a systematic review and meta-analysis involving 1324 samples from 14 separate studies. The overall sensitivity of HRMA was 0.99 (95% confidence interval (CI) = 0.75–0.82), and the overall specificity was very high at 0.99 (95% CI = 0.94–0.98). The values for the pooled positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 68.01 (95% CI = 25.33–182.64), 0.06 (95% CI = 0.03–0.11), and1263.76 (95% CI = 393.91–4064.39), respectively. The summary receiver operating characteristic curve for the same data shows an area of 1.00 and a Q* value of 0.97. The high sensitivity and specificity, simplicity, low cost, less labor or time and rapid turnaround make HRMA a good alternative method for rapid detection of BRAF mutations in the clinical practice.
doi:10.1038/srep04168
PMCID: PMC3933866  PMID: 24566771
4.  Atrophy and Primary Somatosensory Cortical Reorganization after Unilateral Thoracic Spinal Cord Injury: A Longitudinal Functional Magnetic Resonance Imaging Study 
BioMed Research International  2013;2013:753061.
The effects of traumatic spinal cord injury (SCI) on the changes in the central nervous system (CNS) over time may depend on the dynamic interaction between the structural integrity of the spinal cord and the capacity of the brain plasticity. Functional magnetic resonance imaging (fMRI) was used in a longitudinal study on five rhesus monkeys to observe cerebral activation during upper limb somatosensory tasks in healthy animals and after unilateral thoracic SCI. The changes in the spinal cord diameters were measured, and the correlations among time after the lesion, structural changes in the spinal cord, and primary somatosensory cortex (S1) reorganization were also determined. After SCI, activation of the upper limb in S1 shifted to the region which generally dominates the lower limb, and the rostral spinal cord transverse diameter adjacent to the lesion exhibited obvious atrophy, which reflects the SCI-induced changes in the CNS. A significant correlation was found among the time after the lesion, the spinal cord atrophy, and the degree of contralateral S1 reorganization. The results indicate the structural changes in the spinal cord and the dynamic reorganization of the cerebral activation following early SCI stage, which may help to further understand the neural plasticity in the CNS.
doi:10.1155/2013/753061
PMCID: PMC3891744  PMID: 24490171
5.  Two-phase and family-based designs for next-generation sequencing studies 
Frontiers in Genetics  2013;4:276.
The cost of next-generation sequencing is now approaching that of early GWAS panels, but is still out of reach for large epidemiologic studies and the millions of rare variants expected poses challenges for distinguishing causal from non-causal variants. We review two types of designs for sequencing studies: two-phase designs for targeted follow-up of genomewide association studies using unrelated individuals; and family-based designs exploiting co-segregation for prioritizing variants and genes. Two-phase designs subsample subjects for sequencing from a larger case-control study jointly on the basis of their disease and carrier status; the discovered variants are then tested for association in the parent study. The analysis combines the full sequence data from the substudy with the more limited SNP data from the main study. We discuss various methods for selecting this subset of variants and describe the expected yield of true positive associations in the context of an on-going study of second breast cancers following radiotherapy. While the sharing of variants within families means that family-based designs are less efficient for discovery than sequencing unrelated individuals, the ability to exploit co-segregation of variants with disease within families helps distinguish causal from non-causal ones. Furthermore, by enriching for family history, the yield of causal variants can be improved and use of identity-by-descent information improves imputation of genotypes for other family members. We compare the relative efficiency of these designs with those using unrelated individuals for discovering and prioritizing variants or genes for testing association in larger studies. While associations can be tested with single variants, power is low for rare ones. Recent generalizations of burden or kernel tests for gene-level associations to family-based data are appealing. These approaches are illustrated in the context of a family-based study of colorectal cancer.
doi:10.3389/fgene.2013.00276
PMCID: PMC3861783  PMID: 24379824
sequencing; two-phase sampling design; family-based study; rare variant association; breast neoplasms; colorectal cancer
6.  Manual Acupuncture and Laser Acupuncture for Autonomic Regulations in Rats: Observation on Heart Rate Variability and Gastric Motility 
This study focused on the effects of laser acupuncture (LA) and manual acupuncture (MA) at different acupoints on gastric motility and heart rate variability (HRV) simultaneously to elucidate the site specific effects of acupoints and the correlation between changes of gastric motility and low frequency/high frequency (LF/HF) ratio. Gastric motility and HRV were recorded before and during MA or LA. Stimulating PC-6 or ST-36 significantly enhanced gastric motility, while BL-21 caused no changes. In contrast, MA or LA at CV-12 significantly suppressed gastric motility. Stimulating PC-6 or ST-36 significantly increased heart rate (HR), while CV-12 or BL-21 induced no significant changes of HR. Stimulating PC-6 significantly increased LF/HF, while ST-36, CV-12, or BL-21 induced no significant effects. These results indicated that there was acupoint specificity in the effects of acupuncture on gastric motility and HRV. The stimulatory effect of MA and LA at PC-6 and ST-36 on HR was associated with sympathetic activity. The stimulatory effect of MA or LA at PC-6 or ST-36 on gastric motility was associated with vagal activity. Laser needle can be used as an alternative stimulation therapy.
doi:10.1155/2013/276320
PMCID: PMC3857851  PMID: 24348694
7.  Effectiveness of Interstitial Laser Acupuncture Depends upon Dosage: Experimental Results from Electrocardiographic and Electrocorticographic Recordings 
The purpose of this study was to evaluate the influence of the duration of interstitial laser acupuncture therapy effects on neurovegetative and neurobioelectrical parameters like heart rate (HR), heart rate variability (HRV), and electroencephalogram (EEG). We investigated 6 male Sprague-Dawley rats. They underwent 10 min, 20 min, and 30 min interstitial laser acupuncture (in randomized order, with a break of at least 30 min between the different measurement conditions) at the acupoint Neiguan. HR changed significantly only during 20 min red laser stimulation, whereas 10 and 30 min stimulation did not induce significant changes. HRV did not change significantly during any of the different durations; however, an increase was found during 20 min irradiation. Neither the LF/HF ratio of HRV nor the integrated EEG showed significant changes. In this study, it could be experimentally proved that some effects of laser acupuncture are time dependent, and therefore the dosage, as well known from theory, also depends on the time factor. We could especially demonstrate that different treatment times lead to different effects on neurovegetative and neurobioelectrical parameters. Further studies are needed to verify or refute these results.
doi:10.1155/2013/934783
PMCID: PMC3853036  PMID: 24348729
8.  Identification of new HLA-A*0201-restricted cytotoxic T lymphocyte epitopes from neuritin 
Journal of Neuro-Oncology  2013;114:51-58.
Identification of cytotoxic T lymphocyte (CTL) epitopes from additional tumor antigens is essential for the development of specific immunotherapy of malignant tumors. Neuritin, a recently discovered antigen overexpressed in astrocytoma, is considered to be a promising target for biological therapy. In the present study, we predicted and identified HLA-A2-restricted CTL epitopes from neuritin by using the following four-step procedure: (1) computer-based epitope prediction from the amino acid sequence of neuritin; (2) peptide-binding assay to determine the affinity of the predicted peptide with HLA-A2.1 molecule; (3) stimulation of primary T cell response against the predicted peptides in vitro; and (4) testing of the induced CTLs toward target cells expressing neuritin and HLA-A2.1. The results demonstrated that effectors induced by peptides of neuritin containing residues 13–21, 121–129 and 4–12 could specifically-secrete interferon-γ and lyse target cells. Our results indicate that these peptides are new HLA-A2.1-restricted CTL epitopes, and may serve as valuable tools for astrocytoma immunotherapy.
doi:10.1007/s11060-013-1167-6
PMCID: PMC3724992  PMID: 23754640
HLA-A*0201; Cytotoxic T lymphocyte; Epitopes; Neuritin
9.  Splenic siderotic nodules in patients with liver cirrhosis 
The aim of this study was to investigate the interrelation between splenic siderotic nodules, hypersplenism and liver function in patients with liver cirrhosis. The splenic enhanced susceptibility-weighted angiography (ESWAN) and conventional magnetic resonance images of 33 patients with liver cirrhosis were retrospectively studied and the ESWAN images were graded. The distribution and prevalence of the image grades for patients with and without hypersplenism were evaluated. In addition, the splenic volume and the distribution of Child-Pugh and albumin scores were compared between patients with and without siderotic nodules, and the correlation between splenic volume and the ESWAN image grades were evaluated in the patients with siderotic nodules. The ESWAN images revealed splenic siderotic nodules in 24 patients. The distribution and prevalence of the ESWAN image grades were demonstrated to be significantly different (P<0.001) between patients with and without hypersplenism. Furthermore, significant differences were observed between patients with and without siderotic nodules with regard to splenic volume and the distribution of Child-Pugh and serum albumin scores (P<0.001). No significant correlation was demonstrated between splenic volume and the ESWAN image grades (P>0.05). In conclusion, a higher prevalence of splenic siderotic nodules (72.7%) was observed using the ESWAN sequence, in comparison with results from previous studies, obtained using the T1-spoiled gradient echo sequence. The presence of splenic siderotic nodules was consistent with the occurrence of hypersplenism and was interrelated with reserved liver function.
doi:10.3892/etm.2013.1135
PMCID: PMC3786845  PMID: 24137205
spleen; siderotic nodules; magnetic resonance imaging; liver cirrhosis; hypersplenism; thrombocytopenia
10.  Superconductivity at 44 K in K intercalated FeSe system with excess Fe 
Scientific Reports  2013;3:1216.
We report here that a new superconducting phase with much higher Tc has been found in K intercalated FeSe compound with excess Fe. We successfully grew crystals by precisely controlling the starting amount of Fe. Besides the superconducting (SC) transition at ~30 K, we observed a sharp drop in resistivity and a kink in susceptibility at 44 K. By combining thermodynamic measurements with electron spin resonance (ESR), we demonstrate that this is a new SC transition. Structural analysis unambiguously reveals two phases coexisting in the crystals, which are responsible respectively for the SC transitions at 30 and 44 K. The structural experiments and first-principles calculations consistently indicate that the 44 K SC phase is close to a 122 structure, but with an unexpectedly large c-axis of 18.10 Å. We further find a novel monotonic dependence of the maximum Tc on the separation of neighbouring FeSe layers.
doi:10.1038/srep01216
PMCID: PMC3564023  PMID: 23386972
11.  Regulator of G-Protein Signaling–5 Inhibits Bronchial Smooth Muscle Contraction in Severe Asthma 
Severe asthma is associated with fixed airway obstruction attributable to inflammation, copious luminal mucus, and increased airway smooth muscle (ASM) mass. Paradoxically, studies demonstrated that the hypertrophic and hyperplastic ASM characteristic of severe asthma has reduced contractile capacity. We compared the G-protein–coupled receptor (GPCR)–induced Ca2+ mobilization and expression of GPCRs and signaling proteins related to procontractile signaling in ASM derived postmortem from subjects who died of nonrespiratory causes, with cells from subjects who died of asthma. Despite the increased or comparable expression of contraction-promoting GPCRs (bradykinin B2 or histamine H1 and protease-activated receptor 1, respectively) in asthmatic ASM cells relative to cells from healthy donors, asthmatic ASM cells exhibited reduced histamine-induced Ca2+ mobilization and comparable responses to bradykinin and thrombin, suggesting a postreceptor signaling defect. Accordingly, the expression of regulator of G-protein signaling–5 (RGS5), an inhibitor of ASM contraction, was increased in cultured, asthmatic ASM cells and in bronchial smooth muscle bundles of both human subjects with asthma and allergen-challenged mice, relative to those of healthy human subjects or naive mice. The overexpression of RGS5 impaired the release of Ca2+ to thrombin, histamine, and carbachol, and reduced the contraction of precision-cut lung slices to carbachol. These results suggest that increased RGS5 expression contributes to decreased myocyte shortening in severe and fatal asthma.
doi:10.1165/rcmb.2011-0110OC
PMCID: PMC3380291  PMID: 22281988
asthma; bronchial smooth muscle; signal transduction; G-protein–coupled receptors
12.  Melatonin inhibits the expression of vascular endothelial growth factor in pancreatic cancer cells 
Objective
To investigate the effects of melatonin on cellular proliferation and endogenous vascular endothelial growth factor (VEGF) expression in pancreatic carcinoma cells (PANC-1).
Methods
PANC-1 cells were cultured for this study. The secreted VEGF concentration in the culture medium was determined using ELISA method, VEGF production in the tumor cells was detected by immunocytochemistry, and VEGF mRNA expression was determined by RT-PCR.
Results
Higher melatonin concentrations significantly inhibited cellular proliferation, with 1 mmol/L concentration exhibiting the highest inhibitory effect (P<0.01). VEGF concentrations in the cell culture supernatants and intra-cellules were all significantly reduced after melatonin (1 mmol/L) incubation (P<0.05). VEGF mRNA expression decreased markedly in a time-dependent manner during the observation period (P<0.05).
Conclusions
High melatonin concentrations markedly inhibited the proliferation of pancreatic carcinoma cells. The endogenous VEGF expression was also suppressed by melatonin incubation.
doi:10.3978/j.issn.1000-9604.2012.09.03
PMCID: PMC3551319  PMID: 23358453
Melatonin; VEGF; pancreatic cancer
13.  Anaphylaxis and generalized urticaria from eating Chinese bayberry fruit*  
Chinese bayberry myrica rubra is a very popular fruit in southeastern China. In spite of its wide consumption, no allergies to this fruit have been reported previously. Here we report on a 40-year-old woman suffering from anaphylaxis to Chinese bayberry fruit. Prick-prick skin tests revealed strong reactions to fresh Chinese bayberry fruits as well as to peach, and weaker reactions to some other fruits including apple, melon, and banana. ImmunoCAP analysis revealed identical titers of specific IgE (4.3 kUA/L) to peach extract and its lipid transfer protein (LTP, rPru p 3), which was confirmed by detection of a 9 kD band following immunoblotting. Immunoblot analysis with Chinese bayberry extract gave bands of 22, 45, and 90 kD, but no 9 kD band was recognized. There was also no evidence of LTP recognition for loquat (36 kD) or melon (24 kD). This first report of a severe allergic reaction to Chinese bayberry fruit in a patient with LTP-mediated peach allergy indicates that other as yet unidentified non-pollen related fruit allergens are involved in this new severe fruit allergy.
doi:10.1631/jzus.B1200150
PMCID: PMC3468829  PMID: 23024053
Chinese bayberry; Fruit allergy; Anaphylaxis
14.  Ethyl 2-[4-(4-chloro­benzo­yl)phen­oxy]-2-methyl­propano­ate 
In the title compound, C19H19ClO4, the dihedral angle between the mean planes of the benzene rings is 126.8 (1)°. Weak C—H⋯O inter­actions are observed.
doi:10.1107/S1600536812021149
PMCID: PMC3379337  PMID: 22719535
15.  Significance of survivin expression: Prognostic value and survival in stage III non-small cell lung cancer 
This study was designed to determine the levels of survivin expression and identify its clinical significance as a prognostic factor for stage III non-small cell lung cancer (NSCLC). A total of 210 cases of stage III NSCLC were collected and the expression levels of survivin and vascular endothelial growth factor A (VEGF-A) in tumor tissues were investigated using immunohistochemistry (IHC). The medical records of the patients were reviewed to determine the association with clinical course. Of the 210 NSCLC tissues, 112 (53.3%) cases demonstrated positive expression of survivin protein. Coexpression of survivin and VEGF-A was identified. The 5-year survival rate of patients with positive survivin expression was significantly lower compared with the survivin-negative cancer patients (P<0.05). The expression of survivin in NSCLC correlated with tumor size. Survivin and VEGF-A were independent prognostic factors of stage III NSCLC. Survivin protein is a valuable marker of prognosis in stage III NSCLC patients.
doi:10.3892/etm.2012.512
PMCID: PMC3438711  PMID: 22970003
survivin; VEGF-A; immunohistochemistry; prognostic marker
16.  Inhibition airway remodeling and transforming growth factor-β1/Smad signaling pathway by astragalus extract in asthmatic mice 
Airway remodeling is characterized by airway wall thickening, subepithelial fibrosis, increased smooth muscle mass, angiogenesis and increased mucous glands, which can lead to a chronic and obstinate asthma with pulmonary function depression. In the present study, we investigated whether the astragalus extract inhibits airway remodeling in a mouse asthma model and observed the effects of astragalus extract on the transforming growth factor-β1 (TGF-β1)/Smad signaling pathway in ovalbumin-sensitized mice. Mice were sensitized and challenged by ovalbumin to establish a model of asthma. Treatments included the astragalus extract and budesonide. Lung tissues were obtained for hematoxylin and eosin staining and Periodic acid-Schiff staining after the final ovalbumin challenge. Levels of TGF-β1 were assessed by immunohistology and ELISA, levels of TGF-β1 mRNA were measured by RT-PCR, and levels of P-Smad2/3 and T-Smad2/3 were assessed by western blotting. Astragalus extract and budesonide reduced allergen-induced increases in the thickness of bronchial airway and mucous gland hypertrophy, goblet cell hyperplasia and collagen deposition. Levels of lung TGF-β1, TGF-β1 mRNA and P-Smad2/3 were significantly reduced in mice treated with astragalus extract and budesonide. Astragalus extract improved asthma airway remodeling by inhibiting the expression of the TGF-β1/Smad signaling pathway, and may be a potential drug for the treatment of patients with a severe asthma airway.
doi:10.3892/ijmm.2011.868
PMCID: PMC3577142  PMID: 22200784
astragalus plant; airway remodeling; asthma; trans-forming growth factor-β1/Smad signaling pathway
17.  Phosphorylation of RGS13 by the Cyclic AMP-dependent Protein Kinase Inhibits RGS13 Degradation 
Regulators of G-protein signaling (RGS) proteins are scaffolds that control diverse signaling pathways by modulating signalosome formation and by accelerating the GTPase activity of heterotrimeric G proteins. Although expression of many RGS proteins is relatively low in quiescent cells, transcriptional and post-translational responses to environmental cues regulate both their abundance and activity. We found previously that RGS13, one of the smallest RGS proteins in the family, inhibited cyclic AMP-dependent protein kinase (PKA)-induced gene expression through interactions with the transcription factor cAMP-response element-binding (CREB) protein. Here, we show that PKA activation also leads to increased steady-state RGS13 expression through RGS13 phosphorylation, which inhibits RGS13 protein degradation. RGS13 turnover was significantly reduced in cells stimulated with cAMP, which was reversed by expression of the PKA-specific inhibitory peptide PKI. RGS13 phosphorylation was diminished by mutation of an N-terminal Thr residue (T41) identified as a phosphorylation site by mass spectrometry. Mutation of Thr41 in RGS13 to Ala (T41A) reduced steady-state RGS13 levels and its ability to inhibit M2 muscarinic receptor-mediated Erk phosphorylation compared with wild-type RGS13 by attenuating the protective effect of cAMP on RGS13 degradation. RGS13 underwent ubiquitylation, indicating that it is a likely target of the proteasome. These studies are the first to demonstrate post-translational mechanisms controlling the expression of RGS13. Stabilization of RGS13 through PKA-mediated phosphorylation could enhance RGS13 functions, providing negative feedback regulation that promotes cellular desensitization.
doi:10.1093/jmcb/mjq031
PMCID: PMC3031343  PMID: 20974683
RGS proteins; cAMP; protein kinase; phosphorylation
18.  A review of clinical and histological parameters associated with contralateral neck metastases in oral squamous cell carcinoma 
Oral squamous cell carcinoma (OSCC) has a high incidence of cervical micrometastases and sometimes metastasizes contralaterally because of the rich lymphatic intercommunications relative to submucosal plexus of oral cavity that freely communicate across the midline, and it can facilitate the spread of neoplastic cells to any area of the neck consequently. Clinical and histopathologic factors continue to provide predictive information to contralateral neck metastases (CLNM) in OSCC, which determine prophylactic and adjuvant treatments for an individual patient. This review describes the predictive value of clinical-histopathologic factors, which relate to primary tumor and cervical lymph nodes, and surgical dissection and adjuvant treatments. In addition, the indications for elective contralateral neck dissection and adjuvant radiotherapy (aRT) and strategies for follow-up are offered, which is strongly focused by clinicians to prevent later CLNM and poor prognosis subsequently.
doi:10.4248/IJOS11068
PMCID: PMC3469975  PMID: 22010576
oral squamous cell carcinoma; lymph node metastasis; contralateral neck metastasis; neck dissection; head and neck cancer
19.  Polyphosphate Binds to the Principal Sigma Factor of RNA Polymerase during Starvation Response in Helicobacter pylori 
Molecular microbiology  2010;77(3):618-627.
Summary
Helicobacter pylori persists deep in the human gastric mucus layer in a harsh, nutrient-poor environment. Survival under these conditions depends on the ability of this human pathogen to invoke starvation/stress responses when needed. Unlike many bacteria, H. pylori lacks starvation/stress-responding alternative sigma factors, suggesting an additional mechanism might have evolved in this bacterium. H. pylori produces polyphosphate, however, the role and target of polyphosphate during starvation/stress have not been identified. Here we show that polyphosphate accumulated during nutrient starvation directly targets transcriptional machinery by binding to the principal sigma factor in H. pylori, uncovering a novel mechanism in microbial stress response. A positively-charged-Lys-rich region at the NTD of the major sigma factor is identified as the binding region for polyphosphate (region P) in vivo and in vitro, revealing a new element in sigma 70 family proteins. This interaction is biologically significant because mutant strains defective in the interaction undergo premature cell death during starvation. We suggested that polyphosphate is a second messenger employed by H. pylori to mediate gene expression during starvation/stress. The putative “region P” is present in sigma factors of other human pathogens, suggesting that the uncovered interaction might be a general strategy employed by other pathogens.
doi:10.1111/j.1365-2958.2010.07233.x
PMCID: PMC2917625  PMID: 20553390
Helicobacter pylori; Polyphosphate; Sigma factor; Stress responses; Bacterial gene regulation
20.  Gastroesophageal reflux in cirrhotic patients without esophageal varices 
AIM: To evaluate the esophageal motility and abnormal acid and bile reflux incidence in cirrhotic patients without esophageal varices (EV).
METHODS: Seventy-eight patients with liver cirrhosis without EV confirmed by upper gastroesophageal endoscopy and 30 healthy control volunteers were prospectively enrolled in this study. All the patients were evaluated using a modified protocol including Child-Pugh score, upper gastrointestinal endoscopy, esophageal manometry, simultaneous ambulatory 24-h esophageal pH and bilirubin monitoring. All the patients and volunteers accepted the manometric study.
RESULTS: In the liver cirrhosis group, lower esophageal sphincter pressure (LESP, 15.32 ± 2.91 mmHg), peristaltic amplitude (PA, 61.41 ± 10.52 mmHg), peristaltic duration (PD, 5.32 ± 1.22 s), and peristaltic velocity (PV, 5.22 ± 1.11 cm/s) were all significantly abnormal in comparison with those in the control group (P < 0.05), and LESP was negatively correlated with Child-Pugh score. The incidence of reflux esophagitis (RE) and pathologic reflux was 37.18% and 55.13%, respectively (vs control, P < 0.05). And the incidence of isolated abnormal acid reflux, bile reflux and mixed reflux was 12.82%, 14.10% and 28.21% in patients with liver cirrhosis without EV.
CONCLUSION: Cirrhotic patients without EV presented esophageal motor disorders and mixed acid and bile reflux was the main pattern; the cirrhosis itself was an important causative factor.
doi:10.3748/wjg.v17.i13.1753
PMCID: PMC3072641  PMID: 21483637
Gastroesophageal reflux disease; Liver cirrhosis; Esophageal varices; Esophageal manometry; pH; Bilirubin; Monitoring
21.  Significance of CXCR4, phosphorylated STAT3 and VEGF-A expression in resected non-small cell lung cancer 
C-X-C chemokine receptor type 4 (CXCR4) plays an important role in determining the metastatic potential of non-small cell lung cancer. In order to elucidate the effect and mechanism of CXCR4 in tumor angiogenesis we evaluated the clinical significance of CXCR4, phosphorylated signal transducer and activator of transcription 3 (P-STAT3), and vascular endothelial growth factor (VEGF) expression in patients with completely resected non-small cell lung cancer (NSCLC). A total of 208 cases of resected NSCLC were collected, and expression of CXCR4, P-STAT3 and VEGF-A in tumor tissue was investigated using immunohistochemistry (IHC). We reviewed the patient clinical records to determine the association of the expression of these proteins with the clinical course of the disease. Expression of CXCR4, P-STAT3 and VEGF-A was detected in 56.3, 46.2 and 51.9% of the samples, respectively. We observed co-expression between CXCR4, P-STAT3 and VEGF-A. Using multivariate analysis, the expression levels of CXCR4 and VEGF-A were identified as independent prognostic factors that affected overall survival. In conclusion, the results of this study suggest that CXCR4, P-STAT3 and VEGF-A expression may play a role in tumor progression and angiogenesis of NSCLC. However, further studies are needed to uncover the detailed mechanism that underlies the role of these proteins in NSCLC.
doi:10.3892/etm.2011.235
PMCID: PMC3440730  PMID: 22977534
C-X-C chemokine receptor type 4; phosphorylated signal transducer and activator of transcription 3; vascular endothelial growth factor; immunohistochemistry; prognosis; non-small cell lung cancer
22.  Compound and Digenic Heterozygosity Contributes to Arrhythmogenic Right Ventricular Cardiomyopathy 
Objective:
To define the genetic basis of arrhythmogenic right ventricular cardiomyopathy.
Background:
Arrhythmogenic right ventricular cardiomyopathy (ARVC), characterized by right ventricular fibrofatty replacement and arrhythmias, causes sudden death. Autosomal dominant Inheritance, reduced penetrance, and 7 desmosome-encoding causative genes are known. The basis of low penetrance is poorly understood.
Methods:
ARVC probands and family members were enrolled, blood obtained, lymphoblastoid cell lines immortalized, DNA extracted, PCR amplification of desmosome-encoding genes performed, PCR products sequenced and diseased tissue samples studied for intercellular junction protein distribution using confocal immunofluorescence microscopy and antibodies against key proteins.
Results:
We identified 21 variants in plakophilin-2 (PKP2) in 38 of 198 probands (19%), including missense, nonsense, splice site, and deletion/insertion mutations. Pedigrees showed wide intra-familial variability (severe early-onset disease to asymptomatic individuals). In 9/38 probands, PKP2 variants were identified that were encoded in trans (compound heterozygosity). The 38 probands hosting PKP2 variants were screened for other desmosomal genes mutations; second variants (digenic heterozygosity) were identified in 16/38 subjects with PKP2 variants (42%) including desmoplakin (DSP, n=6), desmoglein-2 (DSG2, n=5), plakophilin-4 (PKP4, n=1), and desmocollin-2 (DSC2, n=1). Heterozygous mutations in non-PKP 2desmosomal genes occurred in 14/198 subjects (7%), including DSP (n=4), DSG2 (n=5), DSC2 (n=3), and junctional plakoglobin (JUP, n=2). All variants occurred in conserved regions; none were identified in 700 ethnic-matched controls.
Immunohistochemical analysis demonstrated abnormalities of protein architecture.
Conclusions:
These data suggest that the genetic basis of ARVC includes reduced penetrance with compound and digenic heterozygosity. Disturbed junctional cytoarchitecture in subjects with desmosomal mutations confirms that ARVC is a disease of the desmosome and cell junction.
doi:10.1016/j.jacc.2009.11.020
PMCID: PMC2852685  PMID: 20152563
Arrhythmias; Cardiomyopathies; Desmosomes; Intercalated Disks; Genetic Mutations
23.  Effects of intestinal mucosal blood flow and motility on intestinal mucosa 
AIM: To investigate the role of intestinal mucosal blood flow (IMBF) and motility in the damage of intestinal mucosal barrier in rats with traumatic brain injury.
METHODS: Sixty-four healthy male Wistar rats were divided randomly into two groups: traumatic brain injury (TBI) group (n = 32), rats with traumatic brain injury; and control group (n = 32), rats with sham-operation. Each group was divided into four subgroups (n = 8) as 6, 12, 24 and 48 h after operation. Intestinal motility was measured by the propulsion ratio of a semi-solid colored marker (carbon-ink). IMBF was measured with the laser-Doppler technique. Endotoxin and D-xylose levels in plasma were measured to evaluate the change of intestinal mucosal barrier function following TBI.
RESULTS: The level of endotoxin was significantly higher in TBI group than in the control group at each time point (0.382 ± 0.014 EU/mL vs 0.102 ± 0.007 EU/mL, 0.466 ± 0.018 EU/mL vs 0.114 ± 0.021 EU/mL, 0.478 ± 0.029 EU/mL vs 0.112 ± 0.018 EU/mL and 0.412 ± 0.036 EU/mL vs 0.108 ± 0.011 EU/mL, P < 0.05). D-xylose concentrations in plasma in TBI group were significantly higher than in the control group (6.68 ± 2.37 mmol/L vs 3.66 ± 1.07 mmol/L, 8.51 ± 2.69 mmol /L vs 3.15 ± 0.95 mmol/L, 11.68 ± 3.24 mmol/L vs 3.78 ± 1.12 mmol/L and 10.23 ± 2.83 mmol/L vs 3.34 ± 1.23 mmol/ L, P < 0.05). The IMBF in TBI group was significantly lower than that in the control group (38.5 ± 2.8 PU vs 45.6 ± 4.6 PU, 25.2 ± 3.1 PU vs 48.2 ± 5.3 PU, 21.5 ± 2.7 PU vs 44.9 ± 2.8 PU, 29. 4 ± 3.8 PU vs 46.7 ± 3.2 PU) (P < 0.05). Significant decelerations of intestinal propulsion ratio in TBI groups were found compared with the control group (0.48% ± 0.06% vs 0.62% ± 0.03%, 0.37% ± 0.05% vs 0.64% ± 0.01%, 0.39% ± 0.07% vs 0.63% ± 0.05% and 0.46% ± 0.03% vs 0.65% ± 0.02%) (P < 0.05).
CONCLUSION: The intestinal mucosal permeability is increased obviously in TBI rats. Decrease of intestinal motility and IMBF occur early in TBI, both are important pathogenic factors for stress-related damage of the intestinal mucosal barrier in TBI.
doi:10.3748/wjg.v17.i5.657
PMCID: PMC3040339  PMID: 21350716
Traumatic brain injury; Intestinal mucosa barrier; Stress; Intestinal mucosa blood flow; Intestinal motility
24.  The Aspartate-Semialdehyde Dehydrogenase of Edwardsiella ictaluri and Its Use as Balanced-Lethal System in Fish Vaccinology 
PLoS ONE  2010;5(12):e15944.
asdA mutants of Gram-negative bacteria have an obligate requirement for diaminopimelic acid (DAP), which is an essential constituent of the peptidoglycan layer of the cell wall of these organisms. In environments deprived of DAP, i.e., animal tissues, they will undergo lysis. Deletion of the asdA gene has previously been exploited to develop antibiotic-sensitive strains of live attenuated recombinant bacterial vaccines. Introduction of an Asd+ plasmid into a ΔasdA mutant makes the bacterial strain plasmid-dependent. This dependence on the Asd+ plasmid vector creates a balanced-lethal complementation between the bacterial strain and the recombinant plasmid. E. ictaluri is an enteric Gram-negative fish pathogen that causes enteric septicemia in catfish. Because E. ictaluri is a nasal/oral invasive intracellular pathogen, this bacterium is a candidate to develop a bath/oral live recombinant attenuated Edwardsiella vaccine (RAEV) for the catfish aquaculture industry. As a first step to develop an antibiotic-sensitive RAEV strain, we characterized and deleted the E. ictaluri asdA gene. E. ictaluri ΔasdA01 mutants exhibit an absolute requirement for DAP to grow. The asdA gene of E. ictaluri was complemented by the asdA gene from Salmonella. Several Asd+ expression vectors with different origins of replication were transformed into E. ictaluri ΔasdA01. Asd+ vectors were compatible with the pEI1 and pEI2 E. ictaluri native plasmids. The balanced-lethal system was satisfactorily evaluated in vivo. Recombinant GFP, PspA, and LcrV proteins were synthesized by E. ictaluri ΔasdA01 harboring Asd+ plasmids. Here we constructed a balanced-lethal system, which is the first step to develop an antibiotic-sensitive RAEV for the aquaculture industry.
doi:10.1371/journal.pone.0015944
PMCID: PMC3012122  PMID: 21209920
25.  Impact of residual and intrafractional errors on strategy of correction for image-guided accelerated partial breast irradiation 
Background
The cone beam CT (CBCT) guided radiation can reduce the systematic and random setup errors as compared to the skin-mark setup. However, the residual and intrafractional (RAIF) errors are still unknown. The purpose of this paper is to investigate the magnitude of RAIF errors and correction action levels needed in cone beam computed tomography (CBCT) guided accelerated partial breast irradiation (APBI).
Methods
Ten patients were enrolled in the prospective study of CBCT guided APBI. The postoperative tumor bed was irradiated with 38.5 Gy in 10 fractions over 5 days. Two cone-beam CT data sets were obtained with one before and one after the treatment delivery. The CBCT images were registered online to the planning CT images using the automatic algorithm followed by a fine manual adjustment. An action level of 3 mm, meaning that corrections were performed for translations exceeding 3 mm, was implemented in clinical treatments. Based on the acquired data, different correction action levels were simulated, and random RAIF errors, systematic RAIF errors and related margins before and after the treatments were determined for varying correction action levels.
Results
A total of 75 pairs of CBCT data sets were analyzed. The systematic and random setup errors based on skin-mark setup prior to treatment delivery were 2.1 mm and 1.8 mm in the lateral (LR), 3.1 mm and 2.3 mm in the superior-inferior (SI), and 2.3 mm and 2.0 mm in the anterior-posterior (AP) directions. With the 3 mm correction action level, the systematic and random RAIF errors were 2.5 mm and 2.3 mm in the LR direction, 2.3 mm and 2.3 mm in the SI direction, and 2.3 mm and 2.2 mm in the AP direction after treatments delivery. Accordingly, the margins for correction action levels of 3 mm, 4 mm, 5 mm, 6 mm and no correction were 7.9 mm, 8.0 mm, 8.0 mm, 7.9 mm and 8.0 mm in the LR direction; 6.4 mm, 7.1 mm, 7.9 mm, 9.2 mm and 10.5 mm in the SI direction; 7.6 mm, 7.9 mm, 9.4 mm, 10.1 mm and 12.7 mm in the AP direction, respectively.
Conclusions
Residual and intrafractional errors can significantly affect the accuracy of image-guided APBI with nonplanar 3DCRT techniques. If a 10-mm CTV-PTV margin is applied, a correction action level of 5 mm or less is necessary so as to maintain the RAIF errors within 10 mm for more than 95% of fractions. Pre-treatment CBCT guidance is not a guarantee for safe delivery of the treatment despite its known benefits of reducing the initial setup errors. A patient position verification and correction during the treatment may be a method for the safe delivery.
doi:10.1186/1748-717X-5-96
PMCID: PMC2987941  PMID: 20977723

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